Database Authors
Pallavi Subhraveti1, Peter Midford, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2019 from the annotated genome of Acinetobacter baumannii OIFC074, as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 23.0) [Karp16, Karp11] using MetaCyc version 23.0 [Caspi18]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AMDE0100002427927603269,922RefSeq:NZ_AMDE01000024
NZ_AMDE0100001923622484245,486RefSeq:NZ_AMDE01000019
NZ_AMDE0100005819519023218,705RefSeq:NZ_AMDE01000058
NZ_AMDE0100005516916405177,074RefSeq:NZ_AMDE01000055
NZ_AMDE0100000915915261176,798RefSeq:NZ_AMDE01000009
NZ_AMDE0100004615414653160,206RefSeq:NZ_AMDE01000046
NZ_AMDE0100001014913883155,502RefSeq:NZ_AMDE01000010
NZ_AMDE0100001516816305155,199RefSeq:NZ_AMDE01000015
NZ_AMDE0100003614013064148,481RefSeq:NZ_AMDE01000036
NZ_AMDE0100006314313904144,311RefSeq:NZ_AMDE01000063
NZ_AMDE0100006213112524139,991RefSeq:NZ_AMDE01000062
NZ_AMDE0100003412611925125,416RefSeq:NZ_AMDE01000034
NZ_AMDE0100003212712313123,848RefSeq:NZ_AMDE01000032
NZ_AMDE010000181019704110,754RefSeq:NZ_AMDE01000018
NZ_AMDE010000391099721095,089RefSeq:NZ_AMDE01000039
NZ_AMDE0100004589840591,773RefSeq:NZ_AMDE01000045
NZ_AMDE01000031100944291,203RefSeq:NZ_AMDE01000031
NZ_AMDE0100004474711289,094RefSeq:NZ_AMDE01000044
NZ_AMDE0100006486786288,413RefSeq:NZ_AMDE01000064
NZ_AMDE0100000175711380,855RefSeq:NZ_AMDE01000001
NZ_AMDE0100002383771577,230RefSeq:NZ_AMDE01000023
NZ_AMDE0100006576694374,833RefSeq:NZ_AMDE01000065
NZ_AMDE0100004067660169,059RefSeq:NZ_AMDE01000040
NZ_AMDE0100005961580365,050RefSeq:NZ_AMDE01000059
NZ_AMDE0100003749471153,326RefSeq:NZ_AMDE01000037
NZ_AMDE0100000843400351,276RefSeq:NZ_AMDE01000008
NZ_AMDE0100005058507150,115RefSeq:NZ_AMDE01000050
NZ_AMDE0100004941372242,599RefSeq:NZ_AMDE01000049
NZ_AMDE0100006036350139,866RefSeq:NZ_AMDE01000060
NZ_AMDE0100004839350437,887RefSeq:NZ_AMDE01000048
NZ_AMDE0100004732273237,085RefSeq:NZ_AMDE01000047
NZ_AMDE0100002535331136,819RefSeq:NZ_AMDE01000025
NZ_AMDE0100002832310135,445RefSeq:NZ_AMDE01000028
NZ_AMDE0100004238360234,126RefSeq:NZ_AMDE01000042
NZ_AMDE0100000530281133,350RefSeq:NZ_AMDE01000005
NZ_AMDE0100002631283027,793RefSeq:NZ_AMDE01000026
NZ_AMDE0100005727242126,934RefSeq:NZ_AMDE01000057
NZ_AMDE0100000222200225,236RefSeq:NZ_AMDE01000002
NZ_AMDE0100005124220224,271RefSeq:NZ_AMDE01000051
NZ_AMDE0100001123190423,577RefSeq:NZ_AMDE01000011
NZ_AMDE0100006120170323,008RefSeq:NZ_AMDE01000061
NZ_AMDE0100000722210122,393RefSeq:NZ_AMDE01000007
NZ_AMDE0100003523185020,664RefSeq:NZ_AMDE01000035
NZ_AMDE0100000421140717,058RefSeq:NZ_AMDE01000004
NZ_AMDE0100002024210315,876RefSeq:NZ_AMDE01000020
NZ_AMDE0100002914130115,142RefSeq:NZ_AMDE01000029
NZ_AMDE0100001213110213,160RefSeq:NZ_AMDE01000012
NZ_AMDE0100001716140212,909RefSeq:NZ_AMDE01000017
NZ_AMDE010000211290310,688RefSeq:NZ_AMDE01000021
17 Undisplayed Contigs/Replicons262611730,993
Total:3,8663,627851543,935,888
Ortholog data available?Yes
Database Contents
Genes3,856
Pathways267
Enzymatic Reactions1,299
Transport Reactions114
Polypeptides3,652
Protein Complexes52
Enzymes785
Transporters349
Compounds1,054
Transcription Units2,696
tRNAs63
GO Terms2,166
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii OIFC074
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761203
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903901
Geographic LocationGermany
Collection Date2003-06-2
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-23
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.3
Annotation CommentBest-placed reference protein set; GeneMarkS+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

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